cBioPortal validation report

Study directory:
./generated_data/soft_tissue_tcga_gdc

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 6.0.6

Validation status: Please check
Line Number Column Number Message Value Encountered
Debug – – Requesting info from portal at 'https://www.cbioportal.org' –
Debug – – Requesting cancer-types from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genes from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genesets from portal at 'https://www.cbioportal.org' –
Debug – – Requesting genesets_version from portal at 'https://www.cbioportal.org' –
Debug – – Requesting gene-panels from portal at 'https://www.cbioportal.org' –
Debug – – Retrieving chromosome lengths from '/Users/jko/Code/nci-crdc-pipeline/scripts/importer/chromosome_sizes.json' –
Debug – – Validating case lists –
Info – – Validation of case list folder complete –
Info – – Validation complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 49 1 Clinical data defined for a patient with no samples TCGA-DX-A3LY
Info – – Validation of file complete –
Info – – Read 266 lines. Lines with warning: 1. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Info – – Validation of file complete –
Info – – Read 269 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 86, 177, 178… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1768 values
Info – – Validation of file complete –
Info – – Read 38322 lines. Lines with warning: 1768. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 40784, 57113, 69760 – Segment is zero bases wide and will not be loaded 77760416-77760416, 134773134-134773134, 151721014-151721014
Info – – Validation of file complete –
Info – – Read 128190 lines. Lines with warning: 3. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 87, 193, 194… – Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info – – Validation of file complete –
Info – – Read 40797 lines. Lines with warning: 1899. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 3 – Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view –
Info 4, 14, 15… – Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] Silent, RNA, 5'UTR… See all 4950 values
Warning 749, 882, 1186… – Entrez gene id exists, but gene symbol specified is not known to the cBioPortal instance. The gene symbol will be ignored. Might be wrong mapping, new or deprecated gene symbol. TTC30B, CCDC105, TEX45… See all 46 values
Warning 8654, 9166 – No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag –
Warning 14021, 17256 – Gene symbol not known to the cBioPortal instance. This record will not be loaded. FAM160A2, AL592490.1
Info – – Validation of file complete –
Info – – Read 17408 lines. Lines with warning: 51. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Info – – Validation of file complete –
Info – – Read 265 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Info – – Validation of file complete –
Info – – Read 806 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Warning – – Unrecognized field in meta file short_name
Info – – Validation of meta file complete –
Info – – Setting reference genome to human (GRCh38, hg38) –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script